SGCD
sarcoglycan delta
Basic information
Region (hg38): 5:155870344-156767788
Links
Phenotypes
GenCC
Source:
- autosomal recessive limb-girdle muscular dystrophy type 2F (Definitive), mode of inheritance: AR
- autosomal recessive limb-girdle muscular dystrophy type 2F (Moderate), mode of inheritance: AR
- familial isolated dilated cardiomyopathy (Supportive), mode of inheritance: AD
- autosomal recessive limb-girdle muscular dystrophy type 2F (Supportive), mode of inheritance: AR
- autosomal recessive limb-girdle muscular dystrophy type 2F (Strong), mode of inheritance: AR
- dilated cardiomyopathy 1L (Disputed Evidence), mode of inheritance: AD
- autosomal recessive limb-girdle muscular dystrophy (Definitive), mode of inheritance: AR
- dilated cardiomyopathy (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Cardiomyopathy, dilated, 1L | AR | Cardiovascular | The condition can include severe cardiac manifestations, and knowledge may allow surveillance (eg, with EKG, echocardiogram, and Holter monitoring) and early medical management, which may ameliorate morbidity and mortality; Heart transplantation may be indicated in individuals with severe dilated cardiomyopathy | Cardiovascular; Musculoskeletal | 8841194; 8776597; 10735275; 9832045; 10069710; 10974018,; 18285821; 19259135 |
| Digenic inheritance (with SGCB) has been suggested, but the evidence is unclear |
ClinVar
This is a list of variants' phenotypes submitted to
- Autosomal recessive limb-girdle muscular dystrophy type 2F (16 variants)
- Dilated cardiomyopathy 1L (4 variants)
- not provided (4 variants)
- Dilated cardiomyopathy 1L;Autosomal recessive limb-girdle muscular dystrophy type 2F (2 variants)
- Abnormality of the musculature (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGCD gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 91 | 94 | ||||
| missense | 150 | 155 | ||||
| nonsense | 13 | |||||
| start loss | 1 | |||||
| frameshift | 10 | 19 | ||||
| inframe indel | 4 | |||||
| splice donor/acceptor (+/-2bp) | 18 | |||||
| splice region | 10 | 17 | 27 | |||
| non coding | 140 | 160 | 50 | 350 | ||
| Total | 18 | 21 | 308 | 254 | 53 |
Highest pathogenic variant AF is 0.0000131
Variants in SGCD
This is a list of pathogenic ClinVar variants found in the SGCD region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SGCD | protein_coding | protein_coding | ENST00000337851 | 8 | 897446 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00207 | 0.980 | 124625 | 0 | 12 | 124637 | 0.0000481 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.195 | 144 | 151 | 0.955 | 0.00000775 | 1842 |
| Missense in Polyphen | 44 | 50.692 | 0.86799 | 641 | ||
| Synonymous | -0.181 | 61 | 59.2 | 1.03 | 0.00000318 | 580 |
| Loss of Function | 2.08 | 7 | 15.9 | 0.439 | 9.44e-7 | 187 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000194 | 0.000194 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000467 | 0.0000464 |
| European (Non-Finnish) | 0.0000628 | 0.0000619 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000353 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a link between the F-actin cytoskeleton and the extracellular matrix.;
- Disease
- DISEASE: Limb-girdle muscular dystrophy 2F (LGMD2F) [MIM:601287]: An autosomal recessive degenerative myopathy initially affecting the proximal limb girdle musculature. Muscle from patients shows a complete loss of delta-sarcoglycan as well as of the others components of the sarcoglycan complex. {ECO:0000269|PubMed:9832045}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, dilated 1L (CMD1L) [MIM:606685]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:10974018}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Dilated cardiomyopathy (DCM) - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Arrhythmogenic Right Ventricular Cardiomyopathy
(Consensus)
Recessive Scores
- pRec
- 0.368
Intolerance Scores
- loftool
- 0.276
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.32
Haploinsufficiency Scores
- pHI
- 0.150
- hipred
- Y
- hipred_score
- 0.668
- ghis
- 0.547
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.789
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sgcd
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- sgcd
- Affected structure
- ventricular myocardium
- Phenotype tag
- abnormal
- Phenotype quality
- decreased contractility
Gene ontology
- Biological process
- muscle organ development;cell death;calcium-mediated signaling;cellular protein-containing complex localization;cardiac muscle tissue development;cardiac muscle fiber development;calcium ion homeostasis;heart contraction;coronary vasculature morphogenesis;cardiac muscle cell contraction
- Cellular component
- cytoskeleton;plasma membrane;dystrophin-associated glycoprotein complex;sarcoglycan complex;integral component of membrane;sarcoplasmic reticulum;sarcolemma
- Molecular function